Lists the set of temporary files which will be converted by the network to true temporary file names A comma separated list of global properties which will be automatically exported if this protocol is published as a web service. The path to a protocol that will render an HTML user interface for this protocol. This optional parameter is used by Webport to provide a custom user interface for a protocol. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The component this component is based upon. EmptyProtocol The user who registered this component. Matthew The date this component was registered. Fri Mar 17 00:24:15 2006 Component Comment A top-level component for building protocols. Component Usage The user should customize this description and usage to describe the functioning of their derived protocol. Display Name Test OPTCLUS - Full protocol Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Custom Error Message Component Icon ProtocolNode Component Revision 100 Disabled 0 Protocol Scale 0 GUID {AABAE249-5E6A-436F-B00F-AE6584D9AC33} Component Point 70 -50 By Ref 0 Fancy Help 100 Building protocols in Pipeline Pilot. This is the help window for working with components and protocols in Pipeline Pilot. To create a protocol, drag items from the Components tab into the workspace. Connect them with pipes, edit their parameters, and then click Run to generate results. As you select components and protocols, information about using them is displayed in this help window. The parameters are displayed in the adjacent Parameters window. For more information, go to <a href="javascript:DoLink('scihelpdocs/user/getstart/getstart_intro.htm')">Getting Started with Pipeline Pilot</a>. None None None The server version when this component was registered 5.0.1.100 Runtime Identifier Component Sticky Notes Location of the component in the database. Matthew\Test OPTCLUS - Full protocol Protocol Options Make Shortcut by Default Owner Access Only Protocol Sticky Notes %VERSION 3% 1675 -50 984 696 255 255 0 Example ONLY This is an example protocol which takes an MDL SD file, generates fingerprints and produces a hierarchical clustering. The hierarchy is then analysed to establish the optimum number of clusters to choose. NOTE THAT THIS PROTOCOL IS AN EXAMPLE ONLY, IT WILL NOT RUN WITHOUT THE DIGITAL CHEMISTRY SERVERS BEING INSTALLED ON THE PIPELINE PILOT SERVER martin martin Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:41 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Create WARD Cluster Job Protocol AutoLayout 1 Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {3FAD17C6-E4A1-47B2-8899-64AB5279566F} Component Point 85 -50 Protocol Scale 0 By Ref 0 Fancy Help 100 Create a WARD hierarchical clustering job Creates a WARD clustering job. This allocates a queue entry and returns a jobid and, where key access is required, a key. These are returned as global parameters for the protocol. None Generic Data jobid and key properties for the newly created job Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes %VERSION 3% 475 -50 474 168 255 255 0 Create a WARD based Hierarchical Cluster Job Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Creation\Create WARD Cluster Job Runtime Identifier 0 Protocol Options Make Shortcut by Default Owner Access Only An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. @jobid is defined An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. scitegic/core The date this component was registered. Fri Feb 25 14:43:25 2005 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if job already created Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {DD58ECD1-516F-48FE-A5DB-8328AED680F2} Component Point 85 -50 Fancy Help 100 Filters each data record based on a condition defined as a PilotScript expression. The PilotScript expression provided to the component is evaluated for each incoming data record. The last statement in the expression should evaluate to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. If multiple statements are present, then the value of the last statement is used. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero The server version when this component was registered 4.5.2.200 Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Custom Filter (PilotScript) Runtime Identifier 0:0 The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. createwardjob The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. owner,passwd A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @owner,@password A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Create a new clustering job Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 360 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0:1 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 660 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 0:2 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate @gJobid := jobid; @gOwner := @owner; @gPassword := @password This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:06 2004 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Make jobid, owner and password global The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 0:3 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 935 -50 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The file or URL source to read data\Examples\SampleDrugs.sd The maximum number of data records to read (all if value is empty) 100 A list of properties the reader should retain for each data record that is output. If a value is not defined, retains all properties. If the parameter contains the value "-" (minus sign), properties are not retained. Select True to read the properties for each molecule (in addition to the structures) True False What to call the property that holds the name of each molecule Name The type of tag to create to identify the source of data records. A property called "SourceTag" is created and holds the value indicated. - None: No SourceTag property is created and any existing ones are removed. - Filename: The name of the file read. - FilenameAndExtension: The name of the file read with its file extension. - FullFilename: The name of the file read, including the directory path. - Number: When multiple files are read in this component, they are numbered 1,2,3... - Letter: When multiple files are read in this component, they are lettered A, B, C... - KeepCurrent: Keeps the current value of SourceTag. None Filename FilenameAndExtension FullFilename Number Letter KeepCurrent Useful for reading in query molecules written with the SciTegic SD Writer. To read SciTegic query information contained on the property list of the record, select True. True False What to call the property that holds the comment associated with each molecule When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Delete the file after the data is read [Be Careful!] True False Comment Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files. The user who registered this component. scitegic/chemistry The date this component was registered. Fri Feb 25 14:43:40 2005 Component Usage Creates a molecule data record for each molecule represented in the 'Source' data file. Can read zipped (.zip) and url-based files. Any properties contained in the file will be read into the data records created if the user specifies. Output Pass - Molecule data records Display Name SD Reader Custom Error Message Component Icon DocumentNode GUID {CA65B896-4FE6-4E3A-B884-DC16B53B8D26} The component this component is based upon. SD Reader Disabled 0 Component Point 85 -400 Fancy Help 100 Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files. Creates a molecular data record for each molecule represented in the <I>Source</I> data file. Can read zipped (.zip) and URL-based files. All properties contained in the file are read into the data records. None Molecule Data fields in the SD file will be added to the property fields None Component Sticky Notes The server version when this component was registered 4.5.2.200 Location of the component in the database. Components\Chemistry\Readers\SD Reader Runtime Identifier 1 Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:25 2004 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Create Scitegic fingerprint Protocol AutoLayout 0 Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon CalculatorNode Component Revision 100 The component this component is based upon. SubProtocol GUID {17001C74-63CE-4B4B-B37C-F0EAA19CE4AA} Component Point 360 -400 Protocol Scale 0 By Ref 0 Fancy Help 100 Builds subprotocols in Pipeline Pilot. Use a subprotocol to collapse one or more components into a single item. Open a subprotocol to view or edit its contents. To define input and output ports, right-click and select Edit. You can save subprotocols and reuse them. For more information, see the User Guide help for <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_overview.htm ')">Subprotocols Overview</a>. Tip: Any component can be made into a shortcut, so that the latest version is always used. For more information, see <a href="javascript:DoLink('scihelpdocs/user/subprots/shortcuts.htm ')">Creating Shortcuts</a>. Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol None Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 4.5.1.0 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Components\Generic\Utilities\SubProtocol Utilities\Subprotocol Runtime Identifier 2 Protocol Options Make Shortcut by Default Owner Access Only The type of fingerprint to generate: - ExtendedConnectivity: Generates higher-order features. - Path: Generates higher-order features. ExtendedConnectivity Path MDLPublicKeys UserKeys Method used to assign initial category for atom classes. - AtomType: Uses atom type, charge and hybridization. - ALogPCode: Uses ALogP category of atoms. - FunctionalClass: Uses the following groups: * H-bond acceptor * H-bond donor * Positive ionizable * Negative ionizable * Halogen * Aromatic * None of the above UserAtomTypes - assumes that the property "UserAtomTypes" is defined on the molecule, and contains an array of integers, one for each atom in the molecule. The i'th value in the array is the user atom type for the i'th atom in the molecule. FunctionalClass AtomType ALogPCode UserAtomTypes The maximum bond distance in the substructures represented in the fingerprint. For extended connectivity fingerprints, this is the diameter of the neighborhood surrounding the central atom, and should be an even number. For path fingerprints, this is the maximum number of bonds in the paths. 6 Controls the way the fingerprint is presented: - Fingerprint: A list of the features present in the molecule, with duplicates removed. - Counts: A list of the features present in the molecule, with duplicates retained; if a feature occurs more than once in a molecule, that bit value is included more than once in the output list. Fingerprint Counts Options for the fingerprint calculation. "IncludeStereo" changes the fingerprint. The other options cause the calculation of other properties with associated information. The options are: - IncludeStereo: (#S) include information from stereoatoms into fingerprint calculation. - OutputBitDistance: (#D) output an array with the length or diameter of each bit. - OutputBitSubstructure: (#C) output an array with SMARTS of the fragment example. - OutputBitAllAtoms: (#A) output an array with the set of all atoms involved with a feature anywhere in the molecule. - OutputBitFeatureAtoms: (#F) output an array with the set of atoms showing one example of the feature bit. IncludeStereo OutputBitDistance OutputBitSubstructure OutputBitAllAtoms OutputBitFeatureAtoms Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Comment Calculates a number of different molecular fingerprints, including extended-connectivity fingerprints, daylight-style path fingerprints, and MDL public key fingerprints. The user who registered this component. scitegic/chemistry The date this component was registered. Mon Dec 13 18:41:28 2004 Component Usage 'Type' gives the type of fingerprint we wish to calculate: ExtendedConnectivity generates extended-connectivity fingerprints Path generates Daylight-style path-based fingerprints MDLPublicKeys generates the MDL Public key fingerprints UserKeys generates fingerprints derived from user-defined substructures 'AtomAbstraction' is used by ExtendedConnectivity and Path fingerprints, and defines the abstraction used to generate the initial atom-based codes. 'MaximumDistance' is used by ExtendedConnectivity and Path fingerprints, and gives either the diameter of the neighborhoods considered (if ExtendedConnectivity type) or of the paths (if Path type). Input - Molecule data records Output Pass - Molecule data records augmented with fingerprint information Display Name Create SciTegic fingerprint The component this component is based upon. Molecular Fingerprints Disabled 0 Custom Error Message Component Icon CalculatorNode GUID {C5873CBC-62ED-4F93-A565-13027A5B3512} Component Point 85 -50 Fancy Help 100 Calculates a variety of molecular fingerprints for the input molecules. Uses one the following algorithms to calculate fingerprints <ul> <li>SciTegic extended-connectivity fingerprints <li>Daylight-style path fingerprints <li>MDL public key fingerprints <li>Fingerprints derived from user-defined substructures. These substructure queries are stored in MDL mol or sd query format in "data\Queries\UserQueries". </ul> For both the extended-connectivity and path fingerprints, a number of methods are available to define the atom abstraction used to generate the initial atom code. You should also specify the maximum path distance (such as number of bonds) that will be used to index an individual fragment. For more information on the various fingerprint types, see the User Guide Help Topic <a href="javascript:DoLink('scihelpdocs/user/comps/types/mol_fps_comps.htm')">Molecular Fingerprints</a>. Molecule Molecule Records augmented with the molecular fingerprint property None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Chemistry\Calculators\Molecular Fingerprints Runtime Identifier 0 The name of the property that will contain the source fingerprint information FCFP_6 The expected format of the input property. Available formats are: Fixed-Length Bitset: a bitset or a list of on bits as text, such as "3 4 5". Fixed-Length Binary String: a string such as "0010011". Fixed-Length Hex String: a string such as "3FD54FF". Fixed-Length Array of Bits: an array of zeros and ones. Fixed-Length Array of Counts: an array of zeros and counts. Fixed-Length Base64: a Base64-encoded string of bits. Fixed-Length Daylight Base64: a Daylight Base64-encoded string of bits. List of Integer Bits: an array of the "on" bits. List of Floating-Point Bits: an array of floating-point numbers. List of String Bits: an array of strings. Fixed-Length Bitset Fixed-Length Binary String Fixed-Length Hex String Fixed-Length Array of Bits Fixed-Length Array of Counts Fixed-Length Base64 Fixed-Length Daylight Base64 List of Integer Bits List of Floating-Point Bits List of String Bits The name of the property to save the converted fingerprint into. If left blank, the input property will be overwritten. fingerprint The desired format for the output property. Available formats are: Fixed-Length Bitset: a bitset or a list of on bits as text, such as "3 4 5". Fixed-Length Binary String: a string such as "0010011". Fixed-Length Hex String: a string such as "3FD54FF". Fixed-Length Array of Bits: an array of zeros and ones. Fixed-Length Array of Counts: an array of zeros and counts. Fixed-Length Base64: a Base64-encoded string of bits. Fixed-Length Daylight Base64: a Daylight Base64-encoded string of bits. List of Integer Bits: an array of the "on" bits. List of Floating-Point Bits: an array of floating-point numbers. List of String Bits: an array of strings. Fixed-Length Bitset Fixed-Length Binary String Fixed-Length Hex String Fixed-Length Array of Bits Fixed-Length Array of Counts Fixed-Length Base64 Fixed-Length Daylight Base64 List of Integer Bits List of Floating-Point Bits List of String Bits If the output format is fixed-length, you can specify that length. If the input format is NOT fixed-length, then you MUST specify the length if the output is fixed-length. 1052 When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. scitegic/chemistry The date this component was registered. Mon Dec 13 18:41:31 2004 Component Comment Translates a molecule so that its geometric center lies at the origin. Component Usage Input - Molecular data records Output Pass - Molecular data records with centered coordinates Display Name Convert Fingerprint Custom Error Message Component Icon ComponentNode GUID {88776655-E6CC-49BD-82DA-EBBA9B98C905} Component Point 385 -50 Disabled 0 Fancy Help 100 Converts a property from one fingerprint format and writes a property in a different format. This component is used to convert fingerprint properties to different formats. Typically, SciTegic fingerprints such as FCFP_6 and MDLPublicKeys are a <I>List of Integer Bits</I>. This is useful for preparing externally-generated fingerprints for use in Pipeline Pilot. In that case, you should convert the fingerprints to a useful internal format, such as <I>List of Integer Bits</I>. (This is the SciTegic integer fingerprint format). You can also use this to prepare fingerprints for export to external programs. For example, you may want to convert the fingerprints to a <I>Fixed-Length Array of Bits</I>, which creates an array of a given size, each element either 0 or 1. When fingerprints are shrunk in size, the shrinkage is done by <I>folding</I> the bits using a methematical modulo ("mod") operation. Molecule Data Record with one property containing fingerprint data Molecule Data Record with one property containing fingerprint data and a new property containing the converted fungerprint. None The component this component is based upon Convert Fingerprint The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Chemistry\Manipulators\Convert Fingerprint Runtime Identifier 1 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate changepropertytype(fingerprint, 'String'); This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:06 2004 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Convert bitset to string The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 2 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 635 -50 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The name of the property which contains the fingerprint data. fingerprint The property which contains a unique identifier for the fingerprint. This ID is used to associate fingerprints with cluster members once clustering is finished. cas_rn When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass The type of fingerprint being added. Either <b>onbits</b>, which is a comma separated list of bits which are set in the fingerprint, or <b>binary</b> which is a string of 0 and 1 chars. onbits binary The length of the fingerprint, this is the maximum bit number which can be set, for example if fingerprints are of length 1024 then set this value to 1024. 1052 Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:41 2006 GUID {40835320-4DDF-45BA-BE82-70462221C444} Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Add Fingerprint To Job Protocol AutoLayout 1 Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon DocumentNode Component Revision 100 The component this component is based upon. SubProtocol Component Point 660 -400 Protocol Scale 0 By Ref 0 Fancy Help 100 Adds data from the pipe in the form of a fingerprint to a clustering job Allows fingerprints to be added to a processing job. This is done one fingerprint at a time, with fingerprints being added in one of a number of formats. The fingerprint may be a comma separated list of on-bits, e.g. "1,4,67,898", or a binary list of set and unset bits, e.g. "10010101". The server does not require the fingerprints to have been created in any particular method so long as they adhere to one of the formats shown above. Dataprints and fingerprints cannot be mixed in the same clustering job. Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes %VERSION 3% 1075 -350 451 256 255 255 0 Populate the job with fingerprints created from each structure in an SD file Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Data Addition\Add Fingerprint to Job Runtime Identifier 3 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. adddata The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,id,type,format,maxscreen,data A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,$(FingerprintID),"fp",@Format,$(Length),$(FingerprintData) A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Add data to the job Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 1 The name of the file to use to save the results of the clustering clusresults.txt The delay in seconds between server polls to check if the job is complete Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:41 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Process Cluster Job To Completion Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {D38260CF-DB2E-4B04-B7F9-417734458FB2} Component Point 85 -750 Protocol Scale 0 By Ref 0 Fancy Help 100 Processes a Clustering Job to completion Processes a clustering job previously created using a Create Cluster Job component. The Create job will have passed the global properties @jobid and @key to this component for processing. The job will then run to completion on the server. The component will keep polling the server to see if the job is complete, this may take some time, especially of there are other jobs on the processing queue so ideally it should only be used for small jobs. IMPORTANT If the protocol is stopped for any reason the job will continue to run on the server, it must be stopped separately. None Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Processing\Process Cluster Job To Completion Runtime Identifier 4 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. startjob The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner, passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@Filename A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Cluster the data Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 3:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 3:1 The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. getclusterprogress The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner, passwd A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Get cluster progress Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 660 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 3:2 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate if (progress < 100) then sleep(@Interval * 1000); error('not finished'); end if This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:06 2004 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Check if finished The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 3:3 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 935 -50 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data Generic Data The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The names of properties to remove from each data record entering the component errortext,progress When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal the action to perform Remove The user who registered this component. scitegic/core The date this component was registered. Fri Feb 25 14:43:21 2005 Component Comment Removes the specified properties from the property list. Component Usage 'PropertyList' contains a comma-separated list of the property names that you wish to remove. Input - Data records Output Pass - All Data records Display Name Remove properties Protocol AutoLayout true Protocol ShowComment false Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ExpressionNode Component Revision 100 The component this component is based upon. SubProtocol Protocol Scale 0 Component Point 1235 -50 GUID {C2ED35FF-5397-4877-AADB-10F1A15D60E2} Fancy Help 100 Removes the specified properties. For each data record that enters the component, the specified properties are removed and the modified record is passed out. <p><b>See Also:</b></p> <p><a href="javascript:DoLink('{456195EF-9708-4367-B3DD-21EBF3796604}')">Keep Properties</a>: To keep only a few properties from a long list, it may be more efficient to specify those properties in the <i>Keep Properties</i> component.</p> Generic Data Generic Data Data records with the specified properties removed None The server version when this component was registered 4.5.2.200 Component Sticky Notes By Ref 0 Protocol Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Remove Properties Runtime Identifier 3:4 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 1535 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 3:5 The filename to save the data to dataset_1.dat Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:40 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Save Dataset Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {DF63ACFB-082F-4366-A5FF-C33269C0FA6F} Component Point 360 -750 Protocol Scale 0 By Ref 0 Fancy Help 100 Save Dataset Saves the entire dataset added to a clustering job. This data may then be re-read and added to, or clustered using any of a number of different clustering methods. The format of the dataset file is in either dataprint or fingerprint format. Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Data Load and Save\Save Dataset Runtime Identifier 5 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. savedata The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@filename A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Save data Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 5:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 5:1 The filename to save the partition data hierarchy_1.dat Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:40 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Save Hierarchy Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {348A8AD1-3D31-4C97-9FF5-75B19CC2F66B} Component Point 660 -750 Protocol Scale 0 By Ref 0 Fancy Help 100 Save Hierarchy Saves a hierarchy created from a completed clustering job. Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes %VERSION 3% 1075 -725 467 212 255 255 0 Process the clustering job and save the results and fingerprint data Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Data Load and Save\Save Hierarchy Runtime Identifier 6 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. savehierarchy The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@filename A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Save hierarchy Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 1 martin martin The filename of the dataset which was used to create the hierarchy which will be optimised dataset_1.dat The name of the hierarchy file which was produced after the dataset was clustered hierarchy_1.dat Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:40 2006 GUID {7C59426A-2AE3-4E74-872C-B1CD509BE5AC} Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Create OPTCLUS Cluster Job Protocol AutoLayout 1 Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol Component Point 85 -1100 Protocol Scale 0 By Ref 0 Fancy Help 100 Create an ASSIGN clustering job Creates an assignment clustering job. It uses a previously clustered dataset and allows new items to be assigned to existing clusters. Where the distance of the new structure from the centre of all clusters in the dataset is greater than a given threshold a new cluster is created. The component allocates a queue entry and returns a jobid and, where key access is required, a key. These are returned as global parameters for the protocol. None Generic Data jobid and key properties for the newly created job Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes %VERSION 3% 425 -1025 729 300 0 255 255 Create OPTCLUS Cluster Job and load the dataset and hierarchy from the clustering job thats just finished. This will establish the opimum number of clusters for the dataset Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Creation\Create ASSIGN Cluster Job Runtime Identifier 7 Protocol Options Make Shortcut by Default Owner Access Only An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. @jobid is defined An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. scitegic/core The date this component was registered. Fri Feb 25 14:43:25 2005 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if job already created Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {DD58ECD1-516F-48FE-A5DB-8328AED680F2} Component Point 85 -50 Fancy Help 100 Filters each data record based on a condition defined as a PilotScript expression. The PilotScript expression provided to the component is evaluated for each incoming data record. The last statement in the expression should evaluate to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. If multiple statements are present, then the value of the last statement is used. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero The server version when this component was registered 4.5.2.200 Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Custom Filter (PilotScript) Runtime Identifier 0:0 The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. createoptclusjob The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. owner,passwd A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @owner,@password A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} This is only used when the component is in a batch environment. Comment Enables you to make a SOAP call to a third-party calculator. Display Name Create a new clustering job Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode Component Point 360 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0:1 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 660 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 0:2 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate @gJobid := jobid; @gOwner := @owner; @gPassword := @password This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:06 2004 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Make jobid, owner, password global The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 0:3 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 935 -50 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. loadhierarchy The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@hierarchyfile A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Load hierarchy Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -400 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0:4 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -400 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data None Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 0:5 The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. loaddata The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@datasetfile A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Load dataset Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -750 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 0:6 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -750 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data None Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 0:7 The name of the file to use to save the results of the clustering optclusresults.txt The delay in seconds between server polls to check if the job is complete Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:41 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Process Cluster Job To Completion Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {D38260CF-DB2E-4B04-B7F9-417734458FB2} Component Point 85 -1425 Protocol Scale 0 By Ref 0 Fancy Help 100 Processes a Clustering Job to completion Processes a clustering job previously created using a Create Cluster Job component. The Create job will have passed the global properties @jobid and @key to this component for processing. The job will then run to completion on the server. The component will keep polling the server to see if the job is complete, this may take some time, especially of there are other jobs on the processing queue so ideally it should only be used for small jobs. IMPORTANT If the protocol is stopped for any reason the job will continue to run on the server, it must be stopped separately. None Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Processing\Process Cluster Job To Completion Runtime Identifier 8 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. startjob The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner, passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@Filename A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Cluster the data Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 3:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 3:1 The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. getclusterprogress The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner, passwd A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Get cluster progress Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 660 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 3:2 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate if (progress < 100) then sleep(@Interval * 1000); error('not finished'); end if This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Mon Dec 13 18:41:06 2004 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Check if finished The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 3:3 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 935 -50 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data Generic Data The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The names of properties to remove from each data record entering the component errortext,progress When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal the action to perform Remove The user who registered this component. scitegic/core The date this component was registered. Fri Feb 25 14:43:21 2005 Component Comment Removes the specified properties from the property list. Component Usage 'PropertyList' contains a comma-separated list of the property names that you wish to remove. Input - Data records Output Pass - All Data records Display Name Remove properties Protocol AutoLayout true Protocol ShowComment false Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ExpressionNode Component Revision 100 The component this component is based upon. SubProtocol Protocol Scale 0 Component Point 1235 -50 GUID {C2ED35FF-5397-4877-AADB-10F1A15D60E2} Fancy Help 100 Removes the specified properties. For each data record that enters the component, the specified properties are removed and the modified record is passed out. <p><b>See Also:</b></p> <p><a href="javascript:DoLink('{456195EF-9708-4367-B3DD-21EBF3796604}')">Keep Properties</a>: To keep only a few properties from a long list, it may be more efficient to specify those properties in the <i>Keep Properties</i> component.</p> Generic Data Generic Data Data records with the specified properties removed None The server version when this component was registered 4.5.2.200 Component Sticky Notes By Ref 0 Protocol Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Remove Properties Runtime Identifier 3:4 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 1535 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 3:5 The number of cluster levels to return. 1 Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:40 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Get Optimum Cluster Levels Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {D3EACB9E-E052-433B-B2A4-453B8678EDA7} Component Point 85 -1775 Protocol Scale 0 By Ref 0 Fancy Help 100 Load Hierarchy Loads the results of a hierarchical clustering method such as DivKMeans, Ward or GroupAvg. This hierarchy can then be partitioned and the resulting clusters analysed. None Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Data Load and Save\Load Hierarchy Runtime Identifier 9 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. getoptimumclusterlevels The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,count A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@Count A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Get optimum cluster levels Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. None Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 4:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 4:1 Name of multi-valued property to separate and output as separate records. If multiple properties are given, they each must have the same number of values. If property names are not given, all properties with multiple values are unmerged. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Comment Separates data records containing multiple values into multiple duplicate records each containing only one of the values. The user who registered this component. scitegic/core The date this component was registered. Tue Dec 20 14:14:06 2005 Component Usage Each incoming data record with more than one value in the specified property is duplicated for each of the multiple values. For example, a data object with three values would generate three data objects, each with only one of the three values (but otherwise identical). If no property names are given, then all properties with multiple values are unmerged. If multiple properties are unmerged, they must contain the same number of values. Input - Data records Output Pass - Data records (containing the separated values) Display Name Unmerge Data The component this component is based upon. Unmerge Data Component RunTimeID 4:2 Custom Error Message Component Icon GeneratorNode Disabled 0 GUID {5E28C170-2FEC-4A3C-90A6-2DCEAA330E9D} Component Point 660 -50 Fancy Help 100 Separates data records containing multiple values into multiple duplicate records each containing only one of the values. Each incoming data record with more than one value in the specified properties is duplicated for each of the multiple values. For example, a data object with three values generates three data objects, each with only one of the three values (but otherwise identical). If property names are not given, all properties with multiple values are unmerged. If multiple properties are unmerged, they must contain the same number of values. Generic Data Data records with multiple values for at least one property Generic Data Data records containing the separated values for the property or properties specified. None The server version when this component was registered 5.0.1.100 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Unmerge Data The number of clusters to extract from the hierarchy. This effectively chooses the level of slicing through the dendrogram. $(clusterlevel) Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:42 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Partition a Hierarchy based on optimum Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {80541437-2256-4510-A3CB-5711B36E4620} Component Point 360 -1775 Protocol Scale 0 By Ref 0 Fancy Help 100 Slice a hierarchy to produce a fixed number of clusters. Allows the partitioning of a hierarchy by slicing the dendrogram at a user-chosen level. The user selects the number of clusters required. Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Job Result Processing\Partition a Hierarchy Runtime Identifier 12 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. getpartition The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,numclusters A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,@numclusters A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Get partition from hierarchy Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 7:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 7:1 This expression is executed only the first time data passes into the component. (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) Expression (or list of expressions separated by semi-colons) to evaluate filename := @clusterlevel + "_clusters.dat"; This expression is executed only at finalization (after the last data passes out of the component). (Since there is no data available at finalization time, only expressions referencing global properties are allowed.) Adds any properties calculated in this component to a molecule's property list True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal When TRUE, controls which exit port is used for each data record by evaluating the final expression (or only one) listed in the "Expression" parameter. -Pass (green) port when expression true -Fail (red) port when expression false True False Version of expression parser to use. 2 Comment Processes commands expressed in PilotScript syntax to apply rapid manipulations to data record properties. In this way, the component may be customized to build a new, specialized data manipulation component. The user who registered this component. scitegic/core The date this component was registered. Tue Dec 20 14:14:06 2005 Component Usage The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax. Input - Data records Output Pass - All Data records Display Name Generate filename The component this component is based upon. Custom Manipulator (PilotScript) Component RunTimeID 13 Custom Error Message Component Icon ExpressionNode Disabled 0 GUID {0995D675-7EE2-432C-95DF-E91C14052B22} Component Point 660 -1775 Fancy Help 100 Executes PilotScript to modify data records. Executes custom PilotScript expression(s) for every data record that enters the component. Use this component to build new, specialized data manipulation components. <i>Expression</i> is evaluated for each data record and may alter the properties of the data objects. <i>Initial expression </i> is evaluated the first time data passes into the component and is typically used for initializing global variables. <p><b>See Also:</b></p> <p>For more information, go to <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</p> Generic Data Generic Data None The server version when this component was registered 5.0.1.100 Component Sticky Notes Location of the component in the database. Components\Generic\Manipulators\Custom Manipulator (PilotScript) The filename to save the partition data filename Temporary files converted by the network to true temporary filenames Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols. When the network runs, processes once or until done for each process call True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal The user who registered this component. Matthew The date this component was registered. Thu Mar 16 16:14:40 2006 Component Comment Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it. Component Usage When you are creating a pipeline which requires a subprotocol as a component, you can drag this SubProtocol component into the pipeline, open it, and add components into it. Display Name Save optimum Partition Protocol AutoLayout true Protocol ShowComment true Add Protocol Comment Here Add Protocol Comment Here Disabled 0 Custom Error Message Component Icon ClusteringNode Component Revision 100 The component this component is based upon. SubProtocol GUID {63089188-D7CF-4ED9-8F8B-C811E8B952C0} Component Point 935 -1775 Protocol Scale 0 By Ref 0 Fancy Help 100 Save Partition Allows a partition to be saved once the clustering job has been completed. The file is saved in BCI cluster file format Generic Data Generic Data Records passing out of any unconnected pass ports of components inside the subprotocol Generic Data Records passing out of any unconnected fail ports of components inside the subprotocol The server version when this component was registered 5.0.1.100 Component Sticky Notes %VERSION 3% 1325 -1750 499 212 0 255 255 Get the best number of clusters and save that partition Protocol Sticky Notes Location of the component in the database. Matthew\Digital Chemistry Clustering - OLD\Data Load and Save\Save Partition Runtime Identifier 14 Protocol Options Make Shortcut by Default Owner Access Only The WSDL file that descibes the Web service. The URL that points to the SOAP service. http://$(DC_CLUSTER_SERVER):$(DC_CLUSTER_PORT) The name of the SOAP method to call. savepartition The SOAP method namespace. urn:dcclustersvr A comma-separated list of parameter names that the SOAP method is expecting. jobid,owner,passwd,filename A comma-separated list of parameter values to pass to the method. Each value can be specified as an expression (such as num_atoms + num_bonds, @globalValue). @gJobid,@gOwner,@gPassword,filename A comma-separated list of names that the SOAP method returns. Names of the properties on the data record where the return values of the SOAP method are placed. Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used. The hostname and port in URL form of the HTTP proxy. Example: http://proxy.company.com:8080/ May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may want to disable this option if you are having problems. True False If a response is not received within the specified number of seconds, raises an error. This is only operational when using the HTTP (custom) transport type. When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal This is only used when the component is in a batch environment. The user who registered this component. scitegic/integration The date this component was registered. Mon Dec 13 18:41:50 2004 Comment Enables you to make a SOAP call to a third-party calculator. Display Name Save partition Component Usage This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information. The component this component is based upon. SOAP Method Custom Error Message Component Icon ClusteringNode GUID {6C17DFB2-B879-4FD7-A464-7B5EDFED4F13} Component Point 85 -50 Disabled 0 Fancy Help 100 Enables you to make a SOAP call to a third-party calculator. You can configure this component to make a remote SOAP method call over an intranet or the Internet. A target endpoint is specified; it is the location of the SOAP server that is programmed to receive calls of the name and parameterization specified by this component. For details, see the <a href="javascript:DoLink('scihelpdocs/user/extend/soap/soap_comps.htm')">SOAP component help topics</a> in the User Guide. Generic Data Generic Data None The server version when this component was registered 4.5.1.0 Component Sticky Notes Location of the component in the database. Components\Integration\Application Integrators\SOAP Method Runtime Identifier 9:0 Property the filter will be applied to error An expression evaluated only when the component is first inialized (when the first data record enters). (Since there is no data available at initialization time, only expressions referencing global properties are allowed.) The PilotScript expression used to filter the data. error IS NOT DEFINED; An expression evaluated only when the component is finalized (once the last data record has passed). *Since there is no data available at finalization time, only expressions referencing global properties are allowed. Allows any properties that were calculated in "Expression" to be included with the exiting record. Otherwise, these properties are removed after the evaluation is complete. True False When an recoverable error occurs during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass When an expected data type is not found during processing: Halt: Terminate the execution of the network Fail: Continue execution of the network, passing data out the Fail(red) port Pass: Continue execution of the network, passing data out the Pass(green) port Halt Fail Pass Component Attributes ComponentTakesInput ComponentReturnsPass ComponentReturnsFail ComponentRunsLocal Version of expression parser to use. 2 Comment Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used. The user who registered this component. alizhong The date this component was registered. Fri Apr 25 14:58:35 2003 Component Usage The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Input - Data records Output Pass - Data records which evaluate 'true' Output Fail - Data records which evaluate 'false' Display Name Check if error occurred Custom Error Message Component Icon FilterNode The component this component is based upon. Custom Filter (PilotScript) Disabled 0 GUID {FB8A6B2F-9419-4063-8B0C-59753AACFBC0} Component Point 360 -50 Fancy Help 100 Filters each data record based on whether a property is defined. This component filters each data record based on whether a property is defined. Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port. Generic Data Generic Data Data records for which the final expression in the PilotScript evaluates to True or non-zero Generic Data Data records for which the final expression in the PilotScript evaluates to False or zero Component Sticky Notes Location of the component in the database. Components\Generic\Filters\Property Value Threshold Filter Runtime Identifier 9:1